Alignments for a candidate for mcm-large in Haloglycomyces albus DSM 45210

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Haloglycomyces albus DSM 45210

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_025273936.1 HALAL_RS0110315 methylmalonyl-CoA mutase

Query= BRENDA::O74009
         (563 letters)



>NCBI__GCF_000527155.1:WP_025273936.1
          Length = 576

 Score =  514 bits (1324), Expect = e-150
 Identities = 264/570 (46%), Positives = 375/570 (65%), Gaps = 33/570 (5%)

Query: 17  KRWEETTVKKFLEKAPERKEKFMTDDGFEIKRIYTPADLGEDWNYMEKLGFPGEYPFTRG 76
           KRW++       E A +R   F T  G E+  +Y P + G+D    E++G+PGEYP+TRG
Sbjct: 11  KRWQDR-----YEAARKRDADFTTISGMEVDPLYHPPE-GQDDERFERIGWPGEYPYTRG 64

Query: 77  VYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQTGLSVAFDLPTQLGYDSDHPLAE 136
           +Y T YRGR WT+RQ++G+  A+++N+RYK LL+ G  GLSVAFD+PT +G DSD   + 
Sbjct: 65  LYPTGYRGREWTIRQFSGFGNAKQTNERYKMLLAAGGGGLSVAFDMPTLMGRDSDEAASA 124

Query: 137 GEVGKVGVAIDSLWDMRILFDGIPLDKVSTSMTINSTAANLLAMYILVAEEQGVSQEKLR 196
           GEVG  GVAIDS+ DM ILFDGI L   +TSMTI+  A  +   Y+  AE QG    +L 
Sbjct: 125 GEVGHCGVAIDSVSDMEILFDGINLQDTTTSMTISGPAIPVFCFYLAAAERQGADITQLD 184

Query: 197 GTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAENVPKWNPISISGYHIREAGANAV 256
           GT+Q DI KEYIA+  ++FPP+P +RL  D++ Y +  +P++ P+S+SGYHIREAGA A 
Sbjct: 185 GTLQTDIHKEYIAQKEWLFPPKPHLRLIGDLMEYTSSTIPRYKPLSVSGYHIREAGATAA 244

Query: 257 QEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAKFRAARRLWAYIMK 316
           QE+AFTLADG  YV+  + RG+D +KFAP LSFFF +H +F EEIAKFRAARR+WA  ++
Sbjct: 245 QELAFTLADGFSYVELGLSRGLDPNKFAPGLSFFFDSHIDFFEEIAKFRAARRIWARWLR 304

Query: 317 EWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLHTNSYDEAL 376
           + + A + R+  LRFHTQTAG +LTAQQP NN+VR A++ALAAV+GGT SLHTN+ DE L
Sbjct: 305 DTYGADSERAQWLRFHTQTAGVSLTAQQPYNNVVRTAVEALAAVMGGTNSLHTNALDETL 364

Query: 377 SLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKIQKMG- 435
           +LPTE+S  IALRTQ ++  E+G+ +  DPLGG++Y+E LTD I  +A +   +I  +G 
Sbjct: 365 ALPTEESAEIALRTQAVLRDETGITNVADPLGGSWYVEALTDKIEAQAEEIFRQILALGG 424

Query: 436 -------------------------GMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVG 470
                                    G++R I+ G+    IA++A++YQ+++E+G++ +VG
Sbjct: 425 EVGDADAAEVTKEAFDRHEVGPITTGILRGIDDGWFTSGIADSAFRYQQDLEQGRKHVVG 484

Query: 471 VNAFVTDEPIEVEILKVDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLM 530
           V         E++IL++   +   Q E LK  R++RD   V  +L+ +R A+ +   N++
Sbjct: 485 VTGHTDTVSKELDILRISHEVERDQNELLKDRRAKRDQAAVDASLEDVRTAS-RGSANMI 543

Query: 531 PYIIEAHRHLATLQEVTDVLREIWGEYRAP 560
             I+ A R  ATL E+   L++ WG YR P
Sbjct: 544 EPILNAARREATLGEICGALKDEWGIYREP 573


Lambda     K      H
   0.318    0.134    0.388 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 759
Number of extensions: 34
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 563
Length of database: 576
Length adjustment: 36
Effective length of query: 527
Effective length of database: 540
Effective search space:   284580
Effective search space used:   284580
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources